How are small scale features represented in an Inverse Graphics Network (autoencoder)?
Simply said, there is no specific "meaning" to the features generated. They are simply features that are fitted through math and calculus, and nobody knows what they represent exactly, and will never knows. However we can run PCA (Principal Component Analysis) to see which feature is the most "important" of all, aka which feature affects the most in the output image. Then, you can try adjusting the value to manually see and guess what teh value do, but you will never know what exactly it does as it is an arbitrary feature, not specifically set by the network. One value may mean multiple things, or just things we human don't understand. See this amazing video about this for details:

https://youtu.be/4VAkrUNLKSo

This video explains what PCA does and also an example of the features generated by the network.

For small scales features, they may simply be ignored as they don't contribute much to the loss or accuracy, or maybe they are represented by a big dot or something else until the last few layers. With just 80 features one cannot fully represent a face with such details, and with the resolution the networks like these are trained on, small features like these probably won't be shown in the image.